| Rank | Motif | Name | P-value | log P-pvalue | q-value (Benjamini) | # Target Sequences with Motif | % of Targets Sequences with Motif | # Background Sequences with Motif | % of Background Sequences with Motif | Motif File |
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| 1 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-5 | -1.203e+01 | 0.0023 | 77.0 | 10.38% | 28.1 | 4.22% | motif file (matrix) |
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| 2 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-5 | -1.172e+01 | 0.0023 | 109.0 | 14.69% | 49.6 | 7.45% | motif file (matrix) |
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| 3 |  | Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer | 1e-4 | -1.067e+01 | 0.0030 | 51.0 | 6.87% | 15.2 | 2.28% | motif file (matrix) |
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| 4 |  | Unknown6/Drosophila-Promoters/Homer | 1e-4 | -1.007e+01 | 0.0041 | 44.0 | 5.93% | 12.5 | 1.88% | motif file (matrix) |
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| 5 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-3 | -8.595e+00 | 0.0143 | 56.0 | 7.55% | 21.9 | 3.29% | motif file (matrix) |
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| 6 |  | LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer | 1e-3 | -7.761e+00 | 0.0275 | 52.0 | 7.01% | 20.7 | 3.11% | motif file (matrix) |
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| 7 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-3 | -7.265e+00 | 0.0387 | 137.0 | 18.46% | 81.6 | 12.25% | motif file (matrix) |
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| 8 |  | Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer | 1e-3 | -7.087e+00 | 0.0405 | 211.0 | 28.44% | 140.9 | 21.16% | motif file (matrix) |
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| 9 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-3 | -6.955e+00 | 0.0410 | 59.0 | 7.95% | 26.2 | 3.93% | motif file (matrix) |
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| 10 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-2 | -6.711e+00 | 0.0471 | 97.0 | 13.07% | 53.9 | 8.10% | motif file (matrix) |
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| 11 |  | Unknown2/Drosophila-Promoters/Homer | 1e-2 | -6.641e+00 | 0.0471 | 61.0 | 8.22% | 28.3 | 4.25% | motif file (matrix) |
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| 12 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.634e+00 | 0.0471 | 16.0 | 2.16% | 2.7 | 0.41% | motif file (matrix) |
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| 13 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-2 | -6.222e+00 | 0.0591 | 31.0 | 4.18% | 10.3 | 1.55% | motif file (matrix) |
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| 14 |  | PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer | 1e-2 | -5.243e+00 | 0.1461 | 11.0 | 1.48% | 1.9 | 0.29% | motif file (matrix) |
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| 15 |  | SeqBias: TA-repeat | 1e-2 | -4.723e+00 | 0.2294 | 173.0 | 23.32% | 120.1 | 18.03% | motif file (matrix) |
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| 16 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-2 | -4.685e+00 | 0.2294 | 54.0 | 7.28% | 28.0 | 4.21% | motif file (matrix) |
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| 17 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -4.677e+00 | 0.2294 | 10.0 | 1.35% | 1.5 | 0.22% | motif file (matrix) |
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